Re: [PyMOL] Fwd: contact_map_visualizer pymol plugin
Hi Balaji, you need to upgrade your PyMOL installation. The 0.99rc6 version has a quite old version of python build-in and does not use your python-2.7 installation. Cheers, Thomas On 11/14/2012 06:58 AM, Ban Arn wrote: > Dear Pymol Users > > I am using pymol v-0.99rc6 (in windows). > > I'm trying to install and work on the contact_map_visualizer.py plugin. > > I am using python-2.7and installed all dependecies as mentioned in the > plugin site. > > Initially, I had image module error and later looking into the link > "http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10289.html"; > I sorted out the above error. > > I installed the script using plugin and getting the following error > > *Exception in plugin 'Contact_Map_Visualizer' -- Traceback follows...* > *Traceback (most recent call last):* > * File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pmg_tk\PMGApp.py", line 156, in initialize_plugins* > *__builtin__.__import__(mod_name)* > * File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pmg_tk\startup\Contact_Map_Visualizer.py", line > 291* > * finally:* > * ^* > * SyntaxError: invalid syntax* > *Error: unable to initialize plugin Contact_Map_Visualizer* > > > I tried running the script using the command lines > > run contact_map_visualizer.py >contact_map_visualizer test.png > > and its shows the same error > > *PyMOL>run contact_map_visualizer.py* > *Traceback (most recent call last):* > * File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parser.py", line 285, in parse* > *parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names)* > * File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parsing.py", line 407, in run_file* > *execfile(file,global_ns,local_ns)* > * File "contact_map_visualizer.py", line 291* > * finally:* > * ^* > * SyntaxError: invalid syntax* > > Could you please help me to sort out this error. > > Kindly advice. > > Many Thanks > Balaji -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selecting certain residues within X angs of a point/residue
Hi John, here is something to start with: # put everything in state 1 (convert states to objects) split_states capsid delete capsid # specify the fixed residue select fixedresidue, capsid_0001 and chain D and resi 30 # select residues of interest within given radius select s1, chain A+B+C and resi 23+45+46 select s2, s1 within 40 of fixedresidue # highlight result color blue color yellow, s2 See also: http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators Cheers, Thomas On 11/15/2012 10:47 AM, Jonathan Grimes wrote: > > i am wanting to highlight a number of residues on a virus capsid. i have > 60 > states (objects), and wanted to only select particular residues (say resi > 23,45,46 from 3 chains across all > 60 objects) that are within say 20A or 40A from a fixed point (or > residue). > > could i get advice on what scripts i could use/edit to get this done. > > thanks > jon > > > > Dr. Jonathan M. Grimes, > NDM Senior Reseach Fellow > University Research Lecturer > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > Roosevelt Drive, > Oxford OX3 7BN, UK > > Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Drawing secondary structure for PDB with only Calpha atoms
Hi Jon, this can be done by enabling "cartoon_trace_atoms". set cartoon_trace_atoms show cartoon You can also enable it for your particular object, if you have other objects loaded for which the setting should not apply. set cartoon_trace_atoms, 1, yourcaonlyobject Hope that helps. Cheers, Thomas On 11/15/2012 10:14 AM, Jonathan Grimes wrote: > > I have a pdb file, with only Alpha carbon atoms. > > I want to display the secondary structure. Given that pymol > uses the backbone to define SS elements is there a way > i can draw the cartoon. > > i have tried explicitly defining ss using alter command > but without success. i want to avoid generating the backbone > using an external piece of software. > > thanks > jon > > Dr. Jonathan M. Grimes, > NDM Senior Reseach Fellow > University Research Lecturer > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > Roosevelt Drive, > Oxford OX3 7BN, UK > > Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] selecting certain residues within X angs of a point/residue
i am wanting to highlight a number of residues on a virus capsid. i have 60 states (objects), and wanted to only select particular residues (say resi 23,45,46 from 3 chains across all 60 objects) that are within say 20A or 40A from a fixed point (or residue). could i get advice on what scripts i could use/edit to get this done. thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Drawing secondary structure for PDB with only Calpha atoms
I have a pdb file, with only Alpha carbon atoms. I want to display the secondary structure. Given that pymol uses the backbone to define SS elements is there a way i can draw the cartoon. i have tried explicitly defining ss using alter command but without success. i want to avoid generating the backbone using an external piece of software. thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] assigning secondary strux to artificial AAs
Hi, I was wondering if I have unnatural amino acids in beta sheet mimicking peptides, is there a way to have them show up as a beta sheet in the cartoon representation? I understand the code: alter 1-11/, ss='S' as an example of assigning residues 1-11 as a beta sheet but how do I tackle artificial amino acids. Thanks! -Johnny -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
